There is currently no support for that in the CSS implementation that's integrated into the plugin. The old implementation allowed that but we simplified some things so the conversion process will be fluid.
Since multiple resource files and layered themes are supported internally by Codename One this should probably be easy to accomplish. I'm guessing something like this in the build.xml
might work:
<target name="-cn1-compile-css" if="codename1.cssTheme">
<java jar="${user.home}/.codenameone/designer_1.jar" failonerror="true">
<jvmarg value="-Dcli=true"/>
<arg value="-css"/>
<arg file="css/theme.css"/>
<arg file="src/theme.res"/>
</java>
<java jar="${user.home}/.codenameone/designer_1.jar" failonerror="true">
<jvmarg value="-Dcli=true"/>
<arg value="-css"/>
<arg file="css/second-theme.css"/>
<arg file="src/second-theme.res"/>
</java>
</target>
</project>